diff --git a/README.md b/README.md index 9fefa23..e997646 100644 --- a/README.md +++ b/README.md @@ -1,3 +1,37 @@ # GeneIT -WIP project \ No newline at end of file +WIP project + +## Setup dev env +1. Install prerequisites: + 1. docker + 2. docker-compose + 3. rust + + +2. Start services: +```bash +cd geneit_backend +docker-compose up +``` + + +3. Install Diesel CLI: + +```bash +sudo apt install libpq5 libpq-dev +cargo install diesel_cli --no-default-features --features postgres +``` + + +4. Initialize database: + +```bash +diesel migation run +``` + +> Note: You can access the database directly using this command: +> +> ```bash +> PGPASSWORD=pass psql -h localhost -p 5432 -U user -d bioclimsol +> ``` \ No newline at end of file diff --git a/geneit_backend/.env b/geneit_backend/.env new file mode 100644 index 0000000..1f5789a --- /dev/null +++ b/geneit_backend/.env @@ -0,0 +1 @@ +DATABASE_URL=postgres://user:pass@localhost/geneit diff --git a/geneit_backend/.gitignore b/geneit_backend/.gitignore index af03ac7..4bb3162 100644 --- a/geneit_backend/.gitignore +++ b/geneit_backend/.gitignore @@ -1,2 +1,3 @@ target/ storage/ +.idea \ No newline at end of file diff --git a/geneit_backend/Cargo.lock b/geneit_backend/Cargo.lock new file mode 100644 index 0000000..963d236 --- /dev/null +++ b/geneit_backend/Cargo.lock @@ -0,0 +1,414 @@ +# This file is automatically @generated by Cargo. +# It is not intended for manual editing. +version = 3 + +[[package]] +name = "anstream" +version = "0.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0ca84f3628370c59db74ee214b3263d58f9aadd9b4fe7e711fd87dc452b7f163" +dependencies = [ + "anstyle", + "anstyle-parse", + "anstyle-query", + "anstyle-wincon", + "colorchoice", + "is-terminal", + "utf8parse", +] + +[[package]] +name = "anstyle" +version = "1.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "41ed9a86bf92ae6580e0a31281f65a1b1d867c0cc68d5346e2ae128dddfa6a7d" + +[[package]] +name = "anstyle-parse" +version = "0.2.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e765fd216e48e067936442276d1d57399e37bce53c264d6fefbe298080cb57ee" +dependencies = [ + "utf8parse", +] + +[[package]] +name = "anstyle-query" +version = "1.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "5ca11d4be1bab0c8bc8734a9aa7bf4ee8316d462a08c6ac5052f888fef5b494b" +dependencies = [ + "windows-sys", +] + +[[package]] +name = "anstyle-wincon" +version = "1.0.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "180abfa45703aebe0093f79badacc01b8fd4ea2e35118747e5811127f926e188" +dependencies = [ + "anstyle", + "windows-sys", +] + +[[package]] +name = "bitflags" +version = "1.3.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "bef38d45163c2f1dde094a7dfd33ccf595c92905c8f8f4fdc18d06fb1037718a" + +[[package]] +name = "byteorder" +version = "1.4.3" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "14c189c53d098945499cdfa7ecc63567cf3886b3332b312a5b4585d8d3a6a610" + +[[package]] +name = "cc" +version = "1.0.79" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "50d30906286121d95be3d479533b458f87493b30a4b5f79a607db8f5d11aa91f" + +[[package]] +name = "clap" +version = "4.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "93aae7a4192245f70fe75dd9157fc7b4a5bf53e88d30bd4396f7d8f9284d5acc" +dependencies = [ + "clap_builder", + "clap_derive", + "once_cell", +] + +[[package]] +name = "clap_builder" +version = "4.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4f423e341edefb78c9caba2d9c7f7687d0e72e89df3ce3394554754393ac3990" +dependencies = [ + "anstream", + "anstyle", + "bitflags", + "clap_lex", + "strsim", +] + +[[package]] +name = "clap_derive" +version = "4.3.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "191d9573962933b4027f932c600cd252ce27a8ad5979418fe78e43c07996f27b" +dependencies = [ + "heck", + "proc-macro2", + "quote", + "syn 2.0.16", +] + +[[package]] +name = "clap_lex" +version = "0.5.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2da6da31387c7e4ef160ffab6d5e7f00c42626fe39aea70a7b0f1773f7dd6c1b" + +[[package]] +name = "colorchoice" +version = "1.0.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "acbf1af155f9b9ef647e42cdc158db4b64a1b61f743629225fde6f3e0be2a7c7" + +[[package]] +name = "diesel" +version = "2.0.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "72eb77396836a4505da85bae0712fa324b74acfe1876d7c2f7e694ef3d0ee373" +dependencies = [ + "bitflags", + "byteorder", + "diesel_derives", + "itoa", + "pq-sys", +] + +[[package]] +name = "diesel_derives" +version = "2.0.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "0ad74fdcf086be3d4fdd142f67937678fe60ed431c3b2f08599e7687269410c4" +dependencies = [ + "proc-macro-error", + "proc-macro2", + "quote", + "syn 1.0.109", +] + +[[package]] +name = "errno" +version = "0.3.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4bcfec3a70f97c962c307b2d2c56e358cf1d00b558d74262b5f929ee8cc7e73a" +dependencies = [ + "errno-dragonfly", + "libc", + "windows-sys", +] + +[[package]] +name = "errno-dragonfly" +version = "0.1.2" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "aa68f1b12764fab894d2755d2518754e71b4fd80ecfb822714a1206c2aab39bf" +dependencies = [ + "cc", + "libc", +] + +[[package]] +name = "geneit_backend" +version = "0.1.0" +dependencies = [ + "clap", + "diesel", +] + +[[package]] +name = "heck" +version = "0.4.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "95505c38b4572b2d910cecb0281560f54b440a19336cbbcb27bf6ce6adc6f5a8" + +[[package]] +name = "hermit-abi" +version = "0.3.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fed44880c466736ef9a5c5b5facefb5ed0785676d0c02d612db14e54f0d84286" + +[[package]] +name = "io-lifetimes" +version = "1.0.10" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "9c66c74d2ae7e79a5a8f7ac924adbe38ee42a859c6539ad869eb51f0b52dc220" +dependencies = [ + "hermit-abi", + "libc", + "windows-sys", +] + +[[package]] +name = "is-terminal" +version = "0.4.7" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "adcf93614601c8129ddf72e2d5633df827ba6551541c6d8c59520a371475be1f" +dependencies = [ + "hermit-abi", + "io-lifetimes", + "rustix", + "windows-sys", +] + +[[package]] +name = "itoa" +version = "1.0.6" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "453ad9f582a441959e5f0d088b02ce04cfe8d51a8eaf077f12ac6d3e94164ca6" + +[[package]] +name = "libc" +version = "0.2.144" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "2b00cc1c228a6782d0f076e7b232802e0c5689d41bb5df366f2a6b6621cfdfe1" + +[[package]] +name = "linux-raw-sys" +version = "0.3.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ef53942eb7bf7ff43a617b3e2c1c4a5ecf5944a7c1bc12d7ee39bbb15e5c1519" + +[[package]] +name = "once_cell" +version = "1.17.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b7e5500299e16ebb147ae15a00a942af264cf3688f47923b8fc2cd5858f23ad3" + +[[package]] +name = "pq-sys" +version = "0.4.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "31c0052426df997c0cbd30789eb44ca097e3541717a7b8fa36b1c464ee7edebd" +dependencies = [ + "vcpkg", +] + +[[package]] +name = "proc-macro-error" +version = "1.0.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "da25490ff9892aab3fcf7c36f08cfb902dd3e71ca0f9f9517bea02a73a5ce38c" +dependencies = [ + "proc-macro-error-attr", + "proc-macro2", + "quote", + "syn 1.0.109", + "version_check", +] + +[[package]] +name = "proc-macro-error-attr" +version = "1.0.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a1be40180e52ecc98ad80b184934baf3d0d29f979574e439af5a55274b35f869" +dependencies = [ + "proc-macro2", + "quote", + "version_check", +] + +[[package]] +name = "proc-macro2" +version = "1.0.58" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "fa1fb82fc0c281dd9671101b66b771ebbe1eaf967b96ac8740dcba4b70005ca8" +dependencies = [ + "unicode-ident", +] + +[[package]] +name = "quote" +version = "1.0.27" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "8f4f29d145265ec1c483c7c654450edde0bfe043d3938d6972630663356d9500" +dependencies = [ + "proc-macro2", +] + +[[package]] +name = "rustix" +version = "0.37.19" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "acf8729d8542766f1b2cf77eb034d52f40d375bb8b615d0b147089946e16613d" +dependencies = [ + "bitflags", + "errno", + "io-lifetimes", + "libc", + "linux-raw-sys", + "windows-sys", +] + +[[package]] +name = "strsim" +version = "0.10.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "73473c0e59e6d5812c5dfe2a064a6444949f089e20eec9a2e5506596494e4623" + +[[package]] +name = "syn" +version = "1.0.109" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "72b64191b275b66ffe2469e8af2c1cfe3bafa67b529ead792a6d0160888b4237" +dependencies = [ + "proc-macro2", + "quote", + "unicode-ident", +] + +[[package]] +name = "syn" +version = "2.0.16" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "a6f671d4b5ffdb8eadec19c0ae67fe2639df8684bd7bc4b83d986b8db549cf01" +dependencies = [ + "proc-macro2", + "quote", + "unicode-ident", +] + +[[package]] +name = "unicode-ident" +version = "1.0.8" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "e5464a87b239f13a63a501f2701565754bae92d243d4bb7eb12f6d57d2269bf4" + +[[package]] +name = "utf8parse" +version = "0.2.1" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "711b9620af191e0cdc7468a8d14e709c3dcdb115b36f838e601583af800a370a" + +[[package]] +name = "vcpkg" +version = "0.2.15" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "accd4ea62f7bb7a82fe23066fb0957d48ef677f6eeb8215f372f52e48bb32426" + +[[package]] +name = "version_check" +version = "0.9.4" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "49874b5167b65d7193b8aba1567f5c7d93d001cafc34600cee003eda787e483f" + +[[package]] +name = "windows-sys" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "677d2418bec65e3338edb076e806bc1ec15693c5d0104683f2efe857f61056a9" +dependencies = [ + "windows-targets", +] + +[[package]] +name = "windows-targets" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7b1eb6f0cd7c80c79759c929114ef071b87354ce476d9d94271031c0497adfd5" +dependencies = [ + "windows_aarch64_gnullvm", + "windows_aarch64_msvc", + "windows_i686_gnu", + "windows_i686_msvc", + "windows_x86_64_gnu", + "windows_x86_64_gnullvm", + "windows_x86_64_msvc", +] + +[[package]] +name = "windows_aarch64_gnullvm" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "91ae572e1b79dba883e0d315474df7305d12f569b400fcf90581b06062f7e1bc" + +[[package]] +name = "windows_aarch64_msvc" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "b2ef27e0d7bdfcfc7b868b317c1d32c641a6fe4629c171b8928c7b08d98d7cf3" + +[[package]] +name = "windows_i686_gnu" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "622a1962a7db830d6fd0a69683c80a18fda201879f0f447f065a3b7467daa241" + +[[package]] +name = "windows_i686_msvc" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "4542c6e364ce21bf45d69fdd2a8e455fa38d316158cfd43b3ac1c5b1b19f8e00" + +[[package]] +name = "windows_x86_64_gnu" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "ca2b8a661f7628cbd23440e50b05d705db3686f894fc9580820623656af974b1" + +[[package]] +name = "windows_x86_64_gnullvm" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "7896dbc1f41e08872e9d5e8f8baa8fdd2677f29468c4e156210174edc7f7b953" + +[[package]] +name = "windows_x86_64_msvc" +version = "0.48.0" +source = "registry+https://github.com/rust-lang/crates.io-index" +checksum = "1a515f5799fe4961cb532f983ce2b23082366b898e52ffbce459c86f67c8378a" diff --git a/geneit_backend/Cargo.toml b/geneit_backend/Cargo.toml index b0527b3..9921e9e 100644 --- a/geneit_backend/Cargo.toml +++ b/geneit_backend/Cargo.toml @@ -6,3 +6,5 @@ edition = "2021" # See more keys and their definitions at https://doc.rust-lang.org/cargo/reference/manifest.html [dependencies] +clap = { version = "4.3.0", features = ["derive", "env"] } +diesel = { version = "2.0.4", features = ["postgres"] } \ No newline at end of file diff --git a/geneit_backend/diesel.toml b/geneit_backend/diesel.toml new file mode 100644 index 0000000..35a12ff --- /dev/null +++ b/geneit_backend/diesel.toml @@ -0,0 +1,8 @@ +# For documentation on how to configure this file, +# see https://diesel.rs/guides/configuring-diesel-cli + +[print_schema] +file = "src/schema.rs" + +[migrations_directory] +dir = "migrations" diff --git a/geneit_backend/migrations/.keep b/geneit_backend/migrations/.keep new file mode 100644 index 0000000..e69de29 diff --git a/geneit_backend/migrations/00000000000000_diesel_initial_setup/down.sql b/geneit_backend/migrations/00000000000000_diesel_initial_setup/down.sql new file mode 100644 index 0000000..a9f5260 --- /dev/null +++ b/geneit_backend/migrations/00000000000000_diesel_initial_setup/down.sql @@ -0,0 +1,6 @@ +-- This file was automatically created by Diesel to setup helper functions +-- and other internal bookkeeping. This file is safe to edit, any future +-- changes will be added to existing projects as new migrations. + +DROP FUNCTION IF EXISTS diesel_manage_updated_at(_tbl regclass); +DROP FUNCTION IF EXISTS diesel_set_updated_at(); diff --git a/geneit_backend/migrations/00000000000000_diesel_initial_setup/up.sql b/geneit_backend/migrations/00000000000000_diesel_initial_setup/up.sql new file mode 100644 index 0000000..d68895b --- /dev/null +++ b/geneit_backend/migrations/00000000000000_diesel_initial_setup/up.sql @@ -0,0 +1,36 @@ +-- This file was automatically created by Diesel to setup helper functions +-- and other internal bookkeeping. This file is safe to edit, any future +-- changes will be added to existing projects as new migrations. + + + + +-- Sets up a trigger for the given table to automatically set a column called +-- `updated_at` whenever the row is modified (unless `updated_at` was included +-- in the modified columns) +-- +-- # Example +-- +-- ```sql +-- CREATE TABLE users (id SERIAL PRIMARY KEY, updated_at TIMESTAMP NOT NULL DEFAULT NOW()); +-- +-- SELECT diesel_manage_updated_at('users'); +-- ``` +CREATE OR REPLACE FUNCTION diesel_manage_updated_at(_tbl regclass) RETURNS VOID AS $$ +BEGIN + EXECUTE format('CREATE TRIGGER set_updated_at BEFORE UPDATE ON %s + FOR EACH ROW EXECUTE PROCEDURE diesel_set_updated_at()', _tbl); +END; +$$ LANGUAGE plpgsql; + +CREATE OR REPLACE FUNCTION diesel_set_updated_at() RETURNS trigger AS $$ +BEGIN + IF ( + NEW IS DISTINCT FROM OLD AND + NEW.updated_at IS NOT DISTINCT FROM OLD.updated_at + ) THEN + NEW.updated_at := current_timestamp; + END IF; + RETURN NEW; +END; +$$ LANGUAGE plpgsql; diff --git a/geneit_backend/migrations/2023-05-24-102711_create_users/down.sql b/geneit_backend/migrations/2023-05-24-102711_create_users/down.sql new file mode 100644 index 0000000..f1c3bfb --- /dev/null +++ b/geneit_backend/migrations/2023-05-24-102711_create_users/down.sql @@ -0,0 +1,2 @@ +-- This file should undo anything in `up.sql` +DROP table users; \ No newline at end of file diff --git a/geneit_backend/migrations/2023-05-24-102711_create_users/up.sql b/geneit_backend/migrations/2023-05-24-102711_create_users/up.sql new file mode 100644 index 0000000..187c96e --- /dev/null +++ b/geneit_backend/migrations/2023-05-24-102711_create_users/up.sql @@ -0,0 +1,12 @@ +-- Create table +CREATE TABLE users ( + id SERIAL PRIMARY KEY, + email VARCHAR(255) NOT NULL, + password VARCHAR NULL, + reset_password_token VARCHAR(150) NULL, + time_create BIGINT NOT NULL, + time_gen_reset_token BIGINT NOT NULL DEFAULT 0, + time_activate BIGINT NOT NULL DEFAULT 0, + active BOOLEAN NOT NULL DEFAULT TRUE, + admin BOOLEAN NOT NULL DEFAULT FALSE +) \ No newline at end of file diff --git a/geneit_backend/src/schema.rs b/geneit_backend/src/schema.rs new file mode 100644 index 0000000..a4243e4 --- /dev/null +++ b/geneit_backend/src/schema.rs @@ -0,0 +1,15 @@ +// @generated automatically by Diesel CLI. + +diesel::table! { + users (id) { + id -> Int4, + email -> Varchar, + password -> Nullable, + reset_password_token -> Nullable, + time_create -> Int8, + time_gen_reset_token -> Int8, + time_activate -> Int8, + active -> Bool, + admin -> Bool, + } +}